Author Topic: B.1.1.529 (=omicron)  (Read 272 times)


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B.1.1.529 (=omicron)
« on: November 25, 2021, 11:20:22 pm »

nicd-files :

reports :
daily hosp.:

daily :
dashboard :


weekly hospital admissions
Gauteng,132,127,143,303,821,1130   (1,71,201,827,1130)

'worst-ever' super-mutant Covid variant that will make vaccines at least 40 per cent 'less effective'
South Africa, Namibia, Lesotho, Botswana, Eswatini and Zimbabwe  ; emerged in Botswana

 We estimate that 90% of the cases in Gauteng (at least 1000 a day are this variant,

A57V  ,  del 69-70 , T95I , G142D , del 143-145 , N211I , L212V , RE , V213P , R214E , G339D
S371L , S373P , S375F , K417N , N440K , G445S , S477N , T478K , E484K , Q493R
G496S , Q498R , N501Y , Y505H , T547K , D614G , H655Y , N679K , P681N , N784K
D796Y , N856K , Q954H , N969K , L981F
Code: [Select]
del 69-70
del 143-145

N:del 31-33

orf1ab :
PL:del 1265
nsp6:del 105-107
 available genomes up to 10 mutations apart.

 available genomes up to 10 mutations apart.

“Omicron did not descend from previously identified "variant" viruses and instead,
their closest evolutionary connection is to mid-2020 viruses” writes @trvrb

The WHO has named it "omicron," and classified it as the worst variant yet,
both in transmissibility and virulence.


Dr. Angelique Coetzee, chair of the South African Medical
Association and a practising GP based in Pretoria, said it
was "premature" to make predictions of a health crisis.
"It's all speculation at this stage. It may be it's highly
transmissable but so far the cases we are seeing are
extremely mild," she said.
"Maybe two weeks from now I will have a different opinion
but this is what we are seeing. So are we seriously worried ?
No. We are concerned and we watch what's happening.
But for now we're saying "OK; there's a whole hype out there,
[We're] not sure why."
 Belgium in an unvaccinated young adult woman who developed mild
flu-like symptoms 11 days after travelling to Egypt via Turkey.
Minister of Health Dr Joe Phahlaa
The NICD reported no unusual symptoms have been reported on those infected with
the B.1.1.529 variant, and as with other variants, some people infected with the variant
are asymptomatic as well.

provincial health department of Gauteng gives daily numbers
of cases and hospitalisations
NICD : national infectious ...

Nov 23
#COVID19 UPDATE: A total of 40,791 tests were conducted in the last 24hrs,
with 868 new cases, which represents a 2.1% positivity rate. A further 51#COVID19
related deaths have been reported, bringing total fatalities to 89,635 to date.
See more here:
Nov 22  The @nicd_sa
 has observed an increase in the 7-day moving average for new COVID-19 cases
and the percentage testing positive in Gauteng, particularly in Tshwane
amongst 10 – 29 year old's over the past week. Read more here

Additionally, the NICD has recently identified a cluster amongst the 20 – 44 age
group at an institute of higher education in Tshwane

cases Oct24-Nov27 :
SA-doctor about omicron symptoms :
intense fatigue and a six-year-old child with a very high pulse rate, she said.
None suffered from a loss of taste or smell.
mostly healthy men who turned up “feeling so tired”.
About half of them were unvaccinated.
her patients were all healthy and she was worried the new variant
could still hit older people – with co-morbidities such as diabetes
or heart disease – much harder.
only 30 hospital admissions yesterday !
almost as last week, down from 58,98,60

"We’re seeing a marked change in the demographic profile of patients with COVID-19,”
Rudo Mathivha, head of the intensive care unit at Soweto’s Baragwanath Hospital
Young people, in their 20s to just over their late 30s, are coming in with moderate
to severe disease, some needing intensive care. About 65% are not vaccinated and
most of the rest are only half-vaccinated,”
What looked like a cluster infection among some university students in Pretoria
ballooned into hundreds of new cases and then thousands, first in the capital city
and then to nearby Johannesburg,
said Dr. Graham Snyder, medical director ...
Professor Andrew Pollard, the director of the Oxford Vaccine Group, also said existing
vaccines should work against the new strain,
“It’s extremely unlikely that a reboot of a pandemic in a vaccinated population
like we saw last year (with the Delta variant) is going to happen,” he told BBC radio.

The National Coronavirus Command Council (NCCC) met Saturday to discuss
possible measures, while weighing the impact any moves will have on the
economy, said the people, who asked not to be identified because the talks aren’t public.

40% of vaccinated Malaysians received Sinovac, which has much higher breakthrough
infection risk than Pfizer and AZ.

The two positive #Omicron cases were asymptomatic and fully vaccinated.
They were amongst fourteen people from southern Africa who arrived on Qatar
Airways flight QR908, Doha to Sydney,
Four (4) cases of the new variant, omicron, and all were fully vaccinated.
Boris Johnson says omicron can spread rapidly and affect those who are double vaccinated
South Africa's health minister says on Nov26 , based on a small sample of Omicron cases,
the majority of hospital patients are unvaccinated: "It indicates that the vaccines are
providing protection"

Currently there are around 1.000 confirmed/suspected Omicron cases.
COVID has a hospitalization rate of around 4%, CFR of around 0.8% in some countries.

Drosten geht davon aus, dass Impfstoffe auch gegen omicron schützen.
noch nicht sicher nachgewiesen, dass die neue Variante auch ansteckender ist.
 keine Hinweise darauf, dass das Virus schwerere Krankheitsverläufe auslösen kann
Unterbinden von Flugverbindungen ... gerechtfertigt
 Klaus Stöhr hält Reisebeschränkungen für sinnlos und beruhigt:
Die Impfstoffe wirkten auch gegen mutierte Coronaviren.

Most were men aged under 40. Just under half were vaccinated.
They also had mild muscle aches, a “scratchy throat” and dry cough, she said.
Only a few had a slightly high temperature.
These very mild symptoms were different to other variants,
which gave more severe symptoms.
Coetzee alerted health officials of a “clinical picture that doesn’t fit Delta”
 on November 18, when she received the first seven of her 30-odd patients.

Coetzee - video :

Moderna  chief medical officer Paul Burton said he suspects the new Omicron
coronavirus variant may elude current vaccines, and if so, a reformulated shot
could be available early in 2022.
No new Covid-19 restrictions will be imposed but the government has set up
a task team to explore the possibility of mandatory vaccines,
South African President Cyril Ramaphosa said on Sunday. 2021-11-28
The country will remain on coronavirus alert level 1 for now.
 [because of vaccines]
The ministerial advisory committee has suggested booster doses for the older
 population and those with immunodeficiencies, on the recommendation of doctors.
Ramaphosa said both a fourth wave and new variants were expected by scientists.
health minister Phaahia calls for vaccinations, but no mentioning of evidence that
the vaccine still works
Großbritannien hat wegen der sich ausbreitenden Omikron-Variante des Coronavirus
ein außerplanmäßiges Treffen der G7-Gesundheitsminister einberufen.
Es findert nach Angaben der Regierung in London bereits heute statt.
Barry Schoub, the head of South Africa’s Ministerial Advisory Committee of SA..
“I think what we can be pretty comfortable… that the vaccine will still prevent serious disease,” he said. “That I think we are pretty sure about. How effective it will be in preventing milder disease —
 that we’ve still got to understand.”
On FTN, @ScottGottliebMD says: "If you talk to people in vaccine circles, people who are
working on a vaccine, they have a pretty good degree of confidence that a boosted
vaccine — so, three full doses of vaccine — is going to be fairly protective against
this new variant."
The "vast majority" of Covid-19 patients recently admitted to hospital were unvaccinated,
and most were younger adults

private general practitioner (GP) Dr Unben Pillay told a department of health virtual media
briefing that in the past 10 days, GPs started seeing “a sharp increase in cases of patients
presenting with flu-like symptoms: dry cough, fever, night sweat and general body pains”.

 WHO also weighed in on effectiveness of earlier infection against Omicron, noting that
early evidence suggests an increased risk of reinfection.
the WHO said corticosteroids and IL6 receptor blockers are still effective for treating
patients with severe COVID-19,
« Last Edit: December 16, 2021, 09:26:30 pm by gsgs »

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Re: B.1.1.529 (=omicron)
« Reply #1 on: November 29, 2021, 11:59:56 pm »
That same day, a 36-year-old man left South Africa for Hong Kong, a city with some of the strictest quarantine rules on earth. On Nov. 13, while staying in a designated quarantine hotel, he took a test that confirmed him as one of the earliest cases of Omicron.

Five days later, a 62-year old man staying in the room across the corridor also tested positive. He, too, had the variant, and the genomes of the two samples were so close that one had clearly caught the virus from the other, said Yuen Kwok-yung, an infectious diseases professor at the University of Hong Kong who advises the city’s government on their pandemic response.

CCTV monitors, however, showed that the two men had never met, nor opened their doors at the same time, nor shared any items, and had only contacted hotel personnel in full protective gear, said Prof. Yuen. Most likely, air from one of their hotel rooms spread into the hallway and through a door opening, where the other breathed it in, said Prof. Yuen, who inspected the site using a smoke test.


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Re: B.1.1.529 (=omicron)
« Reply #2 on: November 30, 2021, 01:12:08 am »
weekly hosp : 125,120,135,276,580,71(incomplete)
weekly cases : 593,547,426,737,2762
weekly pos.rates 0.9%,0.9%,0.7%,1.1%,4.3%
9,8,7,3,1,1,1,1,1,0 promille increase yesterday in hosp by age10group

{doesn't look milder than delta from these numbers}
 > Israel is now reporting community transmission of Omicron from a cardiologist
 > with 3 doses to another cardiologist with 3 doses Warning sign

2021-11-30 : 5 omicron sequences at cog-UK
Code: [Select]
B.1.1.529 w=9
      ENG/MILK-2B987AD/2021,Y,2021-11-22,100, B.1.1.529,PLEARN-v1.2.97,0.0,0.9925692411619005,     Omicron (B.1.1.529-like),0.851100,0.000000,X,X,T,A,H,del,Q,L,  orf1ab:K856R, synSNP:C3037T, synSNP:T5386G, synSNP:G5515T, orf1ab:A2710T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:I3758V,synSNP:T13195C, orf1ab:P4715L,synSNP:C15240T, orf1ab:I5967V,        S:A67V,        S:T95I,       S:G339D,       S:S371L,       S:S373P,       S:S375F,       S:S477N,       S:T478K,       S:E484A,       S:Q493R,       S:G496S,       S:Q498R,       S:N501Y,       S:Y505H,       S:T547K,       S:D614G,       S:H655Y,       S:N679K,       S:P681H,       S:N764K,       S:D796Y,       S:N856K,       S:Q954H,       S:N969K,       S:L981F,synSNP:C25000T,synSNP:C25584T,         E:T9I,         M:D3G,        M:Q19E,        M:A63T,synSNP:A27259C,        N:P13L,       N:R203K,       N:G204R,             Y,             G,             A,           ref,             _
      ENG/MILK-2B95A89/2021,Y,2021-11-22,100, B.1.1.529,PLEARN-v1.2.97,0.0,0.9964109466128309,     Omicron (B.1.1.529-like),0.936200,0.000000,X,X,T,A,H,del,Q,L,  orf1ab:K856R, synSNP:C3037T, synSNP:T5386G, orf1ab:T1822I, orf1ab:A2710T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:I3758V,synSNP:T13195C, orf1ab:P4715L,synSNP:C15240T, orf1ab:I5967V,        S:A67V,        S:T95I,       S:G339D,       S:S371L,       S:S373P,       S:S375F,       S:K417N,       S:S477N,       S:T478K,       S:E484A,       S:Q493R,       S:G496S,       S:Q498R,       S:N501Y,       S:Y505H,       S:T547K,       S:D614G,       S:H655Y,       S:N679K,       S:P681H,       S:N764K,       S:D796Y,       S:N856K,       S:Q954H,       S:N969K,       S:L981F,synSNP:C25000T,synSNP:C25584T,         E:T9I,         M:D3G,        M:Q19E,        M:A63T,synSNP:A27259C,        N:P13L,       N:R203K,       N:G204R,             Y,             G,             A,           ref,             _
      ENG/ALDP-2B4DF63/2021,Y,2021-11-20, 99, B.1.1.529,PLEARN-v1.2.97,0.0,0.9925692411619005,     Omicron (B.1.1.529-like),0.851100,0.000000,X,X,T,A,H,del,Q,L,  orf1ab:K856R, synSNP:C3037T, synSNP:T5386G, orf1ab:V1887I, orf1ab:A2710T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:I3758V,synSNP:T13195C, orf1ab:P4715L,synSNP:C15240T, orf1ab:F5086Y, orf1ab:I5967V,        S:A67V,        S:T95I,       S:G339D,       S:S371L,       S:S373P,       S:S375F,       S:S477N,       S:T478K,       S:E484A,       S:Q493R,       S:G496S,       S:Q498R,       S:N501Y,       S:Y505H,       S:T547K,       S:D614G,       S:H655Y,       S:N679K,       S:P681H,       S:N764K,       S:D796Y,       S:N856K,       S:Q954H,       S:N969K,       S:L981F,synSNP:C25000T,synSNP:C25584T,         E:T9I,         M:D3G,        M:Q19E,        M:A63T,synSNP:A27259C,        N:P13L,       N:R203K,       N:G204R,             Y,             G,             A,           ref,             _
      ENG/MILK-2B67570/2021,Y,2021-11-21,100, B.1.1.529,PLEARN-v1.2.97,0.0,0.9925692411619005,     Omicron (B.1.1.529-like),0.851100,0.000000,X,X,T,A,H,del,Q,L,  orf1ab:K856R, synSNP:C3037T, synSNP:T5386G, orf1ab:V1887I, orf1ab:A2710T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:I3758V,synSNP:T13195C, orf1ab:P4715L,synSNP:C15240T, orf1ab:I5967V,        S:A67V,        S:T95I,       S:G339D,       S:S371L,       S:S373P,       S:S375F,       S:S477N,       S:T478K,       S:E484A,       S:Q493R,       S:G496S,       S:Q498R,       S:N501Y,       S:Y505H,       S:T547K,       S:D614G,       S:H655Y,       S:N679K,       S:P681H,       S:N764K,       S:D796Y,       S:N856K,       S:Q954H,       S:N969K,       S:L981F,synSNP:C25000T,synSNP:C25584T,         E:T9I,         M:D3G,        M:Q19E,        M:A63T,synSNP:A27259C,        N:P13L,       N:R203K,       N:G204R,             Y,             G,             A,           ref,             _
     ENG/PHEC-3U06FU0A/2021,N,2021-11-23,100, B.1.1.529,PLEARN-v1.2.97,0.0,0.9247776976688296,     Omicron (B.1.1.529-like),0.680900,0.000000,X,X,T,X,H,del,X,L,  orf1ab:K856R, synSNP:C3037T, synSNP:T5386G, orf1ab:A2710T, orf1ab:T3255I, orf1ab:P3395H, orf1ab:I3758V,synSNP:T13195C, orf1ab:P4715L,synSNP:C15240T, orf1ab:I5967V,        S:A67V,        S:T95I,       S:G339D,       S:T547K,       S:D614G,       S:H655Y,       S:N679K,       S:P681H,       S:N764K,       S:D796Y,       S:N856K,       S:Q954H,       S:N969K,       S:L981F,synSNP:C25000T,synSNP:C25584T,         E:T9I,        M:Q19E,        M:A63T,synSNP:A27259C,        N:P13L,       N:R203K,       N:G204R,             X,             G,             X,           ref,             

Code: [Select]

                                  1  2  3  4  5  6
    1 >Wuhan-Hu1                  0 54 60 54 38 59
    2 >England/MILK-2B987AD/202  54  0  9  4  3 10
    3 >England/MILK-2B95A89/202  60  9  0  9  8  5
    4 >England/MILK-2B67570/202  54  4  9  0  3  6
    5 >England/PHEC-3U06FU0A/202 38  3  8  3  0  8
    6 >England/ALDP-2B4DF63/202  59 10  5  6  8  0
                                  1  2  3  4  5  6

-codon-position---------- 1111 22   2122 21 1 22   2 2 1    2 22  21 1211121 21  1 2  12
1 >Wuhan-Hu1             ................................................................

-codon-position----------1 1111 22   2122 21 1 22   2 2 1    2 22  21 1211121 21  1 2  12

But to explain the current growth rate advantage of Omicron over Delta one already
has to assume almost complete immune evasion even if one assumes an R0 that is
the same as Delta. R0 can't be much less than that of Delta then I would say...
cluster at TUT Nov.18
Head of EU Public Health gives information that thus far
*ALL* (42) Omicron cases in EU are either mild or without symptoms.
On Monday, an NICD presentation a flagged a large number of COVID-19
admissions among infants aged under two years as an area of concern.
But von Gottberg cautioned against linking that with Omicron just yet.
"It looks like in fact some of those admissions might have started before
the emergence of Omicron. We are also seeing that there was an increase
in influenza cases just in the last month or so, and so we need to be really
careful to look at the other respiratory infections," she said.
... a report by Channel 12 said the Pfizer vaccine is just slightly less effective in
preventing infection with Omicron than with Delta – 90% as opposed to 95% –
while it is as effective – around 93% – in preventing serious symptoms at least
for those vaccinated with a booster.

According to the report, the ability of the variant to infect is higher than Delta but
not as much as feared – around 1.3 times higher...
Minimum dose interval for booster jabs to be halved from 6 months to 3
months and all adults to be offered booster Covid vaccine,
UK  Health Secretary  Sajid Javid confirms
So far admissions following ~same path as past waves.
The earliest known cases are still from southern Africa. The first identified samples were
collected Nov. 9, from a 34-year-old man and a 23-year-old man in Johannesburg,
according to the GISAID global database. On Nov. 11, five samples of the variant were
collected in Botswana.

« Last Edit: December 01, 2021, 03:33:48 am by gsgs »


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Re: B.1.1.529 (=omicron)
« Reply #3 on: December 01, 2021, 05:48:49 am »
Botswana :  15 more cases (+4=19)
14 in the Greater Gaborone DHMT area,
4 in the Serowe/Palapye DHMT area, Truck drivers
1 in Kgatleng DHMT   from ZA
3 mild , 12 none  11 vaxed 4 not (asym)
map of the initial omicron-wave in ZA :
On Omicron, for people with prior Covid but unvaccinated:
“In our population…where many people have had previous infection,
we believe that that previous infection doesn’t provide them with
protection from infection due to Omicron”
To Stop a Pandemic - A Better Approach to Global Health Security
cited by 5 :,5&hl=de

what was that organisation, created last year, dedicated to find and stop new outbreaks like omicron ?
Head was Ian Lipkin, I remember how I applauded at twitter. But now I can't find it.
Only nichtssagende stetments by Lipkin now, no reference to that task.

We were asking for it here since 2006's H5N1

China stopped Wuhan-Hu-1 in Feb.2020
But they let it escape to other countries
and most of the rest of the world didn't stop it

Alpha, Delta were detected too late.

Omicron was detected early but spreads better and faster, but i think we should try to stop it to contain it now.,
support ZA's measures financially. Although it's probably invain and too late.
The key to global public health is global cooperation, transparency and investment."
the lack of international, inter-institutional and interpersonal trust, respect and collaboration,
[not the project that I had in mind. It was rather about early stopping emerging pandemics]
Epidemiological data from South Africa shows a 3-fold increase in risk for reinfection
due to Omicron vs. Beta and Delta.
Eine Überstandene Corona-Infektion schützt laut WHO offenbar nicht vor Omikron-Variante
SUBSTANTIAL population-level evidence for evasion of immunity from prior infection

67 omicrons at cog-uk on 1202

« Last Edit: December 03, 2021, 03:49:09 am by gsgs »


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Re: B.1.1.529 (=omicron)
« Reply #4 on: December 03, 2021, 11:40:52 pm »
BioNTech-Chef sieht Notwendigkeit Impfstoff-Anpassung
Risk Assessment for Omicron has been published.
Everything is still uncertain, but it doesn't look good.
first time we've seen data on vaccination status of hospitalised covid patients in Gauteng

vaccination status of in-hospital patients (n=1351) public and private
unknown : 814 ; 190
no : 286 ; 31
yes : 21 ; 9

general wards  ; ICU/HC

VE(hosp)=86% , VE(ICU)=46%(low numbers)

In France the numbers have been inverting for a few months now (then again,
it's winter now over here)
Some regions show up to 76% vaccinated in ICU, despite 94%
vaccination status (12+yo)
What the CDC in Europe reported today is 50% of the cases they've seen outside
South Africa have been asymptomatic, 50% have just presented with mild symptoms,"
says @ScottGottliebMD on Omicron. "The vaccines--seem to be protective against more severe disease."
2021-12-06, 183 confirmed omicron-cases in Denmark
J.Ward estimates the impact of omicron :
Data from @nicd_sa
 show that in Gauteng province, the share of Covid-positive patients in ICU or on
ventilators is somewhere between 2-3x lower than it was at the same stage of
the Delta wave
 In southern New England, it turns out that ~27% of vaccines were given to
previously infected individuals. Pre-print below. 1/
« Last Edit: December 08, 2021, 01:05:21 am by gsgs »


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Re: B.1.1.529 (=omicron)
« Reply #5 on: December 07, 2021, 11:48:51 pm »
Alex Sigal    @sigallab   7h
There are a few results:
1. Omicron still uses ACE2
2. There is a very large drop in neutralization of Omicron by BNT162b2 (2 doses) immunity
relative to ancestral virus
3. Omicron escape from BNT162b2 neutralization is incomplete.
Previous infection + vaccination still neutralizes
 this was better than I expected of Omicron.
Reduction in nAbs was even LESS in those who had a previous infection & two
doses of Pfizer’s vaccine. Boosters should be able to take this on!
right thing to do to switch vaccine between prime and boost
Omicron antibody neutralization thread, with preliminary results, and substantial caveats.
our first results were read this afternoon (1/n).

@CiesekSandra  2021-12-08,06:20UTC
2x Biontech, 2x Moderna, 1xAZ/1x Biontech  nach 6 Monaten 0% Neutralisation bei Omicron,
auch 3x Biontech 3 Monate nach Booster nur 25% NT versus 95% bei Delta.
Bis zu 37fache Reduktion Delta vs. Omicron

Die monoklonalen AK imdevimab und casirivimab sind - wie erwartet- bei Omicron wirkungslos

« Last Edit: December 08, 2021, 02:32:15 am by gsgs »


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Re: B.1.1.529 (=omicron)
« Reply #6 on: December 08, 2021, 10:21:11 pm »
3/4 of Covid patients were in the hospital for other conditions, and only found out they
had Covid-19 upon arrival.
Hospital stays seem considerably shorter (2.8 days, on average) than during
the pre-Omicron pandemic (8.5 days, on average).
24/38 adults in the Covid wards on 2 December, 24 were unvaccinated,
eight had unknown vaccination status and only six had had the jabs.
8/9 of hospitalised for Covid pneumonia,  were unvaccinated
80% of admissions were below the age of 50.
I think it's likely VE against hospitalization will be relatively well-preserved (~50%?)
with 2x vax, increasing to >75% with boost.
I don't expect much VE to be preserved against infection.
sister lineage , BA.1 , BA.2
« Last Edit: December 09, 2021, 03:34:27 am by gsgs »


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Re: B.1.1.529 (=omicron)
« Reply #7 on: December 09, 2021, 10:23:49 pm »
"in the South African city of Tshwane, 70% of those aged 50-69 and 90% of over-80s
had severe cases during the Delta wave. This share is now around 30% for all ages."
2021-12-09 , Alarm as almost 20% of South Africa’s healthcare workers contract Covid
Richard Lessels,
Victor Khanyile, the deputy director of human resources at the department of health,
said there were 72 678 public sector healthcare workers infected as of 6 December,
representing 18% of the entire public healthcare workforce — 403 443 clinical and support staff.
Gauteng, at 17 008, has the highest number of healthcare workers infected followed by
the Eastern Cape with 11 975 and KwaZulu-Natal with 11 246.
shorter-lived than previous variants
update week 48 , comparing hospital surveillance in Tshwane waves 2,3,4

 Selbst Booster scheinen keinen Schutz (oder nur geringen) vor Infektion und leichtem Verlauf zu bieten.
43% with dyspnaea (shortness of breath) despite 3 shots
18/1280=1.4% of Omicron cases in Denmark are hospitalized. Delta was 2%
2021-12-11 : 30% of (COVID)-infections in London are omicron
also thread by Tom Moultre
backlog now, the decrease was not real
Current earliest detection of omicron in South Africa: 8 November, Gauteng
South African president tests positive for Covid-19

1. 2-4 wks after 2nd dose: 56%
2. 3-4 mnths after 2nd dose: 25%


Adults (18+) infected with #Omicron  = 29% less likely to be hospitalised (than with Wuhuan-Hu1)
CDC; Omicron = 2.9% of cases in USA in week 49 , CDC; 13% in NY,NJ
SinoVac doesn’t provide sufficient antibodies to neutralize omicron
HKUMed shows Omicron infects and multiplies 70X faster than Delta in the
human bronchus, which may explain why it transmits faster, BUT also shows
Omicron infection in the lung is significantly LOWER than the original virus,
which may be an indicator of lower disease severity.
« Last Edit: December 15, 2021, 08:14:34 am by gsgs »


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Re: B.1.1.529 (=omicron)
« Reply #8 on: December 19, 2021, 12:23:56 am »
SA , netcare-CEO , 12-13 : it's mild
neue Studie Imperial College, von Lauterbach vor 14h zitiert , als wahrscheinlich eingestuft
"Omnikron tellt alles in den Schatten, was wir bisher in Pandemie gesehen haben"
Katastrophenfall in London ausgerufen
hard lockdown in Netherlands at 2021-12-19, 5 AM
Denmark hospitalisations remain low
Lauterbach schliesst Lockdown ueber Weihnachten aus
Bund und Länder beraten am Dienstag (2021-12-21) über omicron
2021-12-20 , Ireland strengthens lockdown
Denmark re-introduces restrictions
Sachsen verschaeft Corona Massnahmen
in Thueringen ab 2021-12-20
Sobald eine ungeimpfte Person an einem Treffen teilnimmt,
dürfen nur noch zwei Personen aus einem weiteren Haushalt dabei sein.
Bisher galt diese Regel nicht für Geimpfte und Genesene.
Der neue Expertenrat der Bundesregierung spricht sich für Kontaktbeschränkungen "bereits für
die kommenden Tage" aus. Es gehe um "wirksame bundesweit abgestimmte Gegenmaßnahmen",
heißt es in der Stellungnahme, die dem ARD-Hauptstadtstudio vorliegt
 Einschätzung der Wissenschaftler
Bisher sei nicht davon auszugehen, dass im Vergleich zur Delta-Variante Menschen
ohne Immunschutz einen milderen Krankheitsverlauf hätten
It is obvious we are far from 95 per cent effectiveness that we obtained against the initial virus,"
Ugur Sahin told on 2021-12-20
Zoe :    Runny nose,  Headache , Fatigue , Sneezing ,   Sore throat
HALF of patients in London hospitals 'with Covid' were only diagnosed AFTER arriving
with another ailment https://trib.
Chris Whitty : "slightly milder than delta"
Omicron may be ‘intrinsically milder’,  but there is still not yet ‘clear evidence’.
SCOOP: The Omicron coronavirus variant is causing a milder disease than the Delta
strain in most Britons, U.K. government scientists are set to conclude. The U.K.
Health Security Agency is due to publish its early real-world data on the severity
of the disease before Christmas, and Playbook is told the experts are likely to offer
a mixed outlook, with some positives and some negatives
risk of hospitalisation from omicron is 1/3 of the delta risk
new data from @IHME_UW predict nearly 3 billion COVID-19 infections globally
in the next 2 months
« Last Edit: December 22, 2021, 05:01:59 pm by gsgs »


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Re: B.1.1.529 (=omicron)
« Reply #9 on: December 23, 2021, 06:35:29 am »
early omicron severety studies :



vaccine effectiveness



ar:adjusted for reinfections
s: symptomatic disease


 SARS CoV-2 entry into a cell can occur via two routes: one that only needs ACE2 and
another that needs ACE2 and TMPRSS2.
TMPRSS2 (T2) is higher in the lower airways and so virus goes the second route in those areas.
Omicron spike has reduced ability to use the ACE2+T2 route and doesn't respond to higher
T2 levels, unlike Delta

TB33 : risk(EC or hosp,omicron)=0.62*risk(EC,delta)
This effect is still present when stratified by vaccination status

Using a very similar data set, Imperial College, provided estimates that Omicron cases had a 15
to 25% (Hazard ratio 0.8; 95% CI 0.75-85) reduced risk of emergency department attendance
(hospitalisations in their data set) and 40 to 49% (HR 0.55, 95% CI 0.51-59) reduced risk of a
hospitalisation with a stay of one or more nights. Importantly, this group attempt to impute the
effect of prior infection, highlighting that while 17% of the population have tested positive for
COVID-19, this is likely to capture only one-third of total infections that have occurred in
England. Including the likelihood of previous infection, in addition to vaccination in their model,
they have estimated the intrinsic risk difference between Delta and Omicron as between 0 to
30% and the reduced risk of hospitalisation in those previously infected estimated as 55 to 70%.
The Sato Lab (Kei Sato)  @SystemsVirology
Japan - #Omicron is less infectious and pathogenic than #Delta and even an early pandemic
SARS-CoV-2 in infected hamster model. 1/5
Omicron infection enhances neutralizing immunity against Delta
> One of the studies shows omicron is 89% as severe in people with no vax, never infected
Coetzee :
"And their symptoms don't seem to get any worse than that. After about five
days they clear up, and that's it."
Omicron appears to have switched cell entry preference to endosomal fusion
(rather than ACE2+TMPRSS2 mediated cell surface fusion
like previous variants, incl. the well adapted Delta)
Robert Koch Institute report released today states that 95.58% of the #Omicron cases
in Germany are fully vaccinated (28% of those had a "booster"), 4.42% are unvaccinated.
 the 2nd dose mRNA vaccine given to someone who also had past infection
did not further increase antibodies
    Daily modelled estimates produced by the ONS showed around 9.5% of Londoners had
COVID-19 as of Sunday
    Report also showed a record 1 in 35 people in England had COVID-19 between Dec.
13 and Dec. 19
The ONS report also showed a record 1 in 35 people in England had COVID-19 between Dec. 13 and Dec. 19 — compared with a previous estimate published on Thursday of 1 in 45 in the week to Dec. 16.
7% infected in London during Christmas
Study estimates nation’s Omicron outbreak grew 70% in a week to hit one in 25 people – as data shows infections are now rising quickest in over-65s

The Office for National Statistics swabbing estimates that 2.03 million people had the virus
on any given day in the week before Christmas
2022-01-01 ,
The ONS conducts weekly surveillance tests
2022-01-04 , Neil Ferguson warns of 5,000 Omicron deaths a DAY in UK
ahh, seems to be old news (I had missed it)
Published: 15:38 GMT, 17 December 2021 | Updated: 23:58 GMT, 17 December 2021
 new projections show that daily estimated #COVID19 infections has peaked at 6.2 million
on 1/6 in the US, but daily cases will rise to nearly 1.2 million by 1/19, 2022.
80-90% asymptomatic
intrinsically reduced virulence may account for an approx 25%

« Last Edit: January 13, 2022, 04:03:33 am by gsgs »


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Re: B.1.1.529 (=omicron)
« Reply #10 on: December 27, 2021, 09:09:53 pm »
London, admissions dec06-jan09

London, in hospital dec06-jan11
(max. was 7840)
boroughs :

2022-01-02 : ZOE COVID Study shows infections in London dropping
 and appear to have reached an R rate of 1.0. 

2022-01-08 :
The median R-value across England is below 1 (0.98) Also true in East, London, SE, NW and E Midlands, although NE England is on 1.3

Denmark, 1216-0110    (max was 964 on 2021-01-04)

NY, in hospital, 11-22 ... 01-09

Israel, cases , Nov29-Jan03
 766, 684, 443, 565, 415, 359, 473,
 755, 804, 755, 571, 585, 356, 474,
 800, 761, 627, 878, 720, 696, 794,

Israel, positive-rate Nov29-Jan02

Ontario , VE(case),1129-1231

Ontario , VE(hosp),1213-1231

in hospital in 51 US-States , change last 3 weeks , and number per M. population in the last 22 days
Code: [Select]
OH,106, 97,119,,510,502,491,475,462,436,423,428,432,439,439,442,430,427,437,436,434,433,437,424,414,410
IN,108, 95,103,,440,443,442,440,442,433,425,424,416,433,425,436,431,430,443,441,439,442,427,426,426,410
MI, 92, 83,112,,409,401,390,380,380,371,361,365,373,387,382,406,407,415,435,446,456,465,469,471,465,470
PA,101, 95,120,,405,403,384,369,357,346,335,335,340,343,352,349,347,347,352,354,357,357,360,349,345,346
WV,103, 94,117,,400,374,375,382,355,335,332,340,330,339,344,354,363,376,358,355,362,368,367,363,362,346
WI,100, 93,109,,322,321,317,310,299,284,284,293,297,304,307,313,306,308,313,315,310,319,307,316,318,310
AZ, 92, 92, 96,,319,322,324,318,327,325,323,329,341,342,348,355,349,346,354,359,375,380,386,375,376,384
KY,105, 96,118,,318,318,318,318,295,271,268,268,268,268,268,267,267,278,278,278,274,277,269,278,264,264
KS,109, 96,116,,313,303,303,267,281,267,263,269,273,281,280,275,273,278,280,276,272,266,251,256,255,256
NH,101, 81,102,,290,290,290,286,294,301,283,283,283,283,306,327,324,347,347,347,347,354,349,339,343,343
NV, 97,101,129,,283,283,283,252,254,240,218,218,218,218,217,225,214,214,214,214,218,226,222,212,220,220
NE, 96, 79,107,,270,272,267,256,247,240,238,251,262,256,279,268,292,297,317,311,328,338,320,320,325,328
SD, 89, 96, 97,,259,268,271,266,256,258,266,265,275,268,269,269,256,263,275,281,298,299,320,307,304,307
ME,103, 88, 93,,253,248,254,250,261,264,261,272,281,290,308,309,309,309,306,309,306,306,297,293,287,296
MN, 90, 94, 94,,250,250,249,255,258,265,265,265,265,268,266,274,278,278,279,290,294,304,309,309,310,310
IA, 98, 90,107,,249,252,236,236,226,228,225,232,237,239,240,246,249,258,257,263,286,265,260,261,257,261
NM, 89, 88, 94,,242,242,242,222,218,215,257,257,257,257,264,261,254,291,291,312,289,289,314,288,326,326
FL,107,150,232,,242,229,205,178,146,111,106,104,101, 88, 85, 76, 70, 70, 69, 70, 72, 72, 65, 65, 64, 64
MS,104,112,204,,221,209,195,164,143,110,108,108,102,104,107, 99, 93, 95, 96,100,102,124, 95, 89, 90, 92
AR,108, 90,138,,214,207,194,194,189,172,160,155,163,164,164,164,170,171,171,178,175,171,172,169,161,157
CO, 87, 87,111,,206,206,201,201,197,187,184,184,184,187,187,190,211,211,211,211,218,222,228,231,240,240
SC,113,108,165,,202,191,168,160,132,121,121,122,122,114,109,104,108,110,112,111,116,113,108, 98, 99, 99
AL,115,110,209,,176,157,143,121,105,105, 74, 84, 86, 85, 82, 78, 76, 72, 76, 74, 75, 73, 71, 68, 66, 66
LA,102,147,250,,163,163,163,141,110, 96, 65, 65, 65, 65, 58, 56, 51, 44, 44, 44, 42, 43, 42, 42, 43, 43
CA,103,101,160,,160,147,139,131,120,111,105,100,102,101,100, 97, 97, 97, 99, 99,100, 99, 99, 96, 96, 96
ND, 84, 78,114,,157,163,163,138,139,133,137,137,148,155,152,154,180,178,175,187,201,202,209,211,211,206
WA, 99, 98,125,,143,143,126,124,112, 98,116,114,115,115, 95,105,111,111,116,112,115,129,110,116,117,117
UT, 94, 83,114,,143,136,135,133,131,130,127,125,125,133,134,131,146,147,149,155,152,159,154,154,155,157
ID, 90, 81,107,,134,134,133,135,127,121,120,125,130,129,134,140,151,151,154,161,161,166,167,171,173,171
WY, 90, 76, 84,,116,114,114,128,112,138,138,138,138,138,142,142,142,180,180,171,171,183,187,199,199,199
HI,117,148,186,,114,110,103, 86, 74, 58, 59, 61, 52, 49, 44, 45, 39, 38, 41, 34, 34, 31, 34, 35, 34, 35
MT, 80, 81,108,,113,113,113,111,111,103,104,104,104,104,115,117,116,128,128,128,140,140,143,151,160,160
OR, 96, 89,132,,110,110,110,104, 98, 93, 83, 83, 83, 83, 82, 83, 85, 93, 93, 93, 97, 96, 96,101, 96, 96
VT, 73, 94,106,, 87, 87, 87, 83, 85, 96, 82, 82, 82, 82, 82, 85, 85, 91, 87, 93, 93,108,119,119,111,118
AK, 79, 86, 93,, 74, 74, 74, 74, 80, 80, 79, 79, 79, 79, 79, 95, 95, 91, 91, 91, 98, 98, 92, 92,115,115
01, 02, 03, 04,  05, 06,... , 26

the 26 columns are :

02,100 * (in_hospital_dec18) / (in_hospital_dec11)
03,100 * (in_hospital_dec25) / (in_hospital_dec18)
04,100 * (in_hospital_jan01) / (in_hospital_dec25)
05, in_hospital_per_million_population_jan01
06, in_hospital_per_illion_population_dec31

(in_hospital always means  : in_hospital_with_COVID )

(MO=Missouri removed - to_be_corrected)

data from newsnodes
click "show hospital data"

charts for this , update 0108 :

the hospital trend is about 5 days behind the cases-trend ,
but more reliable especially on weekends and holidays


charts for this :


South Africa , weekly cases,hospitalisations and deaths by week of occurance :

« Last Edit: January 20, 2022, 09:01:28 am by gsgs »